Thesis (Ph.D., Plant, Soil and Entomological Sciences)--University of Idaho, June 2014 | Bean common mosaic virus (BCMV) exists as a complex of strains, which have been classified into seven pathogroups. These BCMV strains and strains of the closely related Bean common mosaic necrosis virus (BCMNV) can be distinguished based on their biological, molecular and serological properties. Seven resistance genes govern interactions of common beans (Phaseolus vulgaris) and BCMV/BCMNV strains: one dominant I gene, and six recessive genes, bc-u, bc-1 and an allelic bc-12, bc-2 and an allelic bc-22, and bc-3. Prior to this work, virus genetic determinants involved in pathogenicity interactions of BCMV with resistance genes were not identified or mapped. Here, we conducted a systematic study of biological and molecular properties of a group of field-collected and reference BCMV isolates in order to identify genetic determinants involved in interactions with three recessive genes, bc-1, bc-2, and bc-22, and the dominant I gene. Through comparative genomics of four closely related BCMV isolates from the RU1 strain group, and three other BCMV strains, US1, US10, and NY15P, putative genetic determinants interacting with recessive genes, bc-1, bc-2, and bc-22, as well as the dominant I gene in P. vulgaris were identified and mapped to the P1 and HC-Pro regions. Genome diversity we found in this study suggested BCMV strains represented multiple recombinants, and the occurrence of recombination in BCMV genome may or may not lead to pathogenicity changes. Due to the wide spread of recombination in BCMV strains, partial sequencing cannot be a reliable means of BCMV strain classification.